{ "area_vx2": 647187.5, "base_shape_zyx": [ 18946, 8174, 8174 ], "bbox": [ [ 5589.39892578125, 4279.662109375, 15836.689453125 ], [ 5859.36767578125, 4885.8681640625, 17042.765625 ] ], "extra_channels": [ { "dtype": "float32", "file": "flow_gate_local_contrast.tif", "name": "flow_gate_local_contrast", "range": [ 0.0, 1.0 ], "source": "pred_dt_flow_gate.local_contrast", "source_config": { "backtrack_distance": 50.0, "gate_factor": 1.0, "grid_step": 4, "local_boost": 0.5 } }, { "dtype": "float32", "file": "flow_gate_component_normalized.tif", "name": "flow_gate_component_normalized", "range": [ 0.0, 1.0 ], "source": "pred_dt_flow_gate.component_normalized", "source_config": { "backtrack_distance": 50.0, "gate_factor": 1.0, "grid_step": 4, "local_boost": 0.5 } } ], "fit_config": { "_corr_point_roi_init_": { "effective_seed": [ 23122.212890625, 18300.66796875, 66058.90625 ], "final_anchor_h": 383.9999999701977, "final_anchor_w": 43.35642513632774, "final_shell_id": "shell_0007.tifxyz", "final_trim_bottom": 28, "final_trim_top": 0, "init_margin_grid_points": 80, "initial_seed": [ 23135.267578125, 18304.103515625, 65910.0859375 ], "initial_shell_id": "shell_0007.tifxyz", "initial_skipped_point_count": 0, "initial_skipped_reasons": {}, "initial_trim_bottom": 28, "initial_trim_top": 0, "initial_usable_point_count": 17, "mode": "corr-point-roi", "model_h": 8576.327514648438, "model_w": 8165.856552124023, "model_w_unit": "voxels", "output_radius_grid_points": 20, "parsed_point_count": 17, "projected_h_span_grid": 11.52655029296875, "projected_h_span_vx": 576.3275146484375, "projected_points": [ { "collection_id": 985, "direction_sign": 1, "grid_distance_to_anchor": 6.333048565855712, "h": 377.7759704589844, "point_id": 117115, "row_index": 0, "w": 44.526451110839844 }, { "collection_id": 985, "direction_sign": -1, "grid_distance_to_anchor": 6.568412356718264, "h": 377.5848388671875, "point_id": 117116, "row_index": 1, "w": 44.76700973510742 }, { "collection_id": 985, "direction_sign": -1, "grid_distance_to_anchor": 6.138104528518454, "h": 378.05474853515625, "point_id": 117117, "row_index": 2, "w": 44.88296127319336 }, { "collection_id": 985, "direction_sign": -1, "grid_distance_to_anchor": 5.519513145463231, "h": 378.6497802734375, "point_id": 117118, "row_index": 3, "w": 44.712955474853516 }, { "collection_id": 985, "direction_sign": -1, "grid_distance_to_anchor": 4.6433805850679, "h": 379.51434326171875, "point_id": 117119, "row_index": 4, "w": 44.55636978149414 }, { "collection_id": 985, "direction_sign": -1, "grid_distance_to_anchor": 4.359927146333566, "h": 379.8677673339844, "point_id": 117120, "row_index": 5, "w": 44.746971130371094 }, { "collection_id": 985, "direction_sign": -1, "grid_distance_to_anchor": 3.1002901967036913, "h": 381.114990234375, "point_id": 117121, "row_index": 6, "w": 44.491554260253906 }, { "collection_id": 985, "direction_sign": 1, "grid_distance_to_anchor": 2.180685178971909, "h": 381.9946594238281, "point_id": 117122, "row_index": 7, "w": 44.21316146850586 }, { "collection_id": 985, "direction_sign": 1, "grid_distance_to_anchor": 0.28841729996161225, "h": 384.0645446777344, "point_id": 117123, "row_index": 8, "w": 43.63752746582031 }, { "collection_id": 985, "direction_sign": -1, "grid_distance_to_anchor": 0.08479031394781394, "h": 383.9579162597656, "point_id": 117124, "row_index": 9, "w": 43.43003463745117 }, { "collection_id": 985, "direction_sign": -1, "grid_distance_to_anchor": 0.2388574893983755, "h": 384.2328796386719, "point_id": 117125, "row_index": 10, "w": 43.303321838378906 }, { "collection_id": 985, "direction_sign": -1, "grid_distance_to_anchor": 1.419209164264935, "h": 385.3376159667969, "point_id": 117126, "row_index": 11, "w": 42.88214874267578 }, { "collection_id": 985, "direction_sign": 1, "grid_distance_to_anchor": 3.3814564154901543, "h": 387.3206787109375, "point_id": 117127, "row_index": 12, "w": 42.71819305419922 }, { "collection_id": 985, "direction_sign": -1, "grid_distance_to_anchor": 2.3066260230354794, "h": 386.2377624511719, "point_id": 117128, "row_index": 13, "w": 42.79701232910156 }, { "collection_id": 985, "direction_sign": -1, "grid_distance_to_anchor": 3.0512080858423687, "h": 386.76385498046875, "point_id": 117129, "row_index": 14, "w": 42.06376266479492 }, { "collection_id": 985, "direction_sign": -1, "grid_distance_to_anchor": 3.970789679488789, "h": 387.67919921875, "point_id": 117130, "row_index": 15, "w": 41.862884521484375 }, { "collection_id": 985, "direction_sign": -1, "grid_distance_to_anchor": 5.415951400007132, "h": 389.11138916015625, "point_id": 117131, "row_index": 16, "w": 41.56583023071289 } ], "projected_w_span_grid": 3.3171310424804688, "projected_w_span_vx": 165.85655212402344, "projection_mode": "normal-line", "skipped_point_count": 0, "skipped_points": [], "skipped_reasons": {}, "usable_point_count": 17, "windings": 1 }, "args": { "approval-inpaint": false, "approval-inpaint-corr-spacing": null, "approval-inpaint-output-mask": false, "approval-inpaint-output-mask-dilate": 3, "approval-inpaint-padding-frac": 0.25, "approval-inpaint-tifxyz": null, "corr-point-roi": true, "corr-point-roi-init-margin": 80, "corr-point-roi-output-radius": 20, "crop": null, "cuda-gridsample": 1, "depth": 1, "device": "cuda", "downscale": 4.0, "erode-valid-mask": 0, "flatten-solver": "torch", "init-mode": "shell-dir-crop", "input": "/ephemeral/lasag_strip_outputs/.lasagna_point_strip_work/collection_985/point_strip.lasagna.json", "mesh-h": 32, "mesh-step": 50, "mesh-w": 32, "model-h": 8576.327514648438, "model-init": "seed", "model-input": null, "model-output": "/tmp/fit_reopt_4uf6zhkn/model_reopt.pt", "model-w": 8165.856552124023, "model-w-unit": "voxels", "normal-mask-zero": 0, "out-dir": null, "progress": true, "pyramid-d": false, "seed": [ 23122.212890625, 18300.66796875, 66058.90625 ], "snapshot-interval": 1000, "sparse-prefetch-backend": "tensorstore", "subsample-mesh": 4, "subsample-winding": 4, "tifxyz-flow-gate-channels": true, "tifxyz-init": null, "winding-step": 25, "winding-volume": null, "windings": 1, "z-center": 0.0 }, "base": { "bend": 100.0, "corr": 0.0001, "data": 0.0, "data_plain": 0.0, "ext_offset": 0.0, "normal": 1.0, "pred_dt": 0.001, "smooth": 10.0, "station_n": 0.1, "station_t": 0.1, "step": 10.0, "winding_density": 0.01 }, "corr_points": { "collections": { "985": { "color": [ 0.250980406999588, 1.0, 0.6274510025978088 ], "metadata": { "winding_is_absolute": true }, "name": "same_wrap2691", "points": { "117115": { "creation_time": 1779714836375, "p": [ 23324.5546875, 18353.939453125, 64593.921875 ], "wind_a": 0.0 }, "117116": { "creation_time": 1779714836375, "p": [ 23324.5546875, 18353.939453125, 64673.921875 ], "wind_a": 0.0 }, "117117": { "creation_time": 1779714836375, "p": [ 23298.4453125, 18347.06640625, 64822.7421875 ], "wind_a": 0.0 }, "117118": { "creation_time": 1779714836375, "p": [ 23263.33984375, 18337.822265625, 64967.703125 ], "wind_a": 0.0 }, "117119": { "creation_time": 1779714836375, "p": [ 23223.16015625, 18327.244140625, 65110.4921875 ], "wind_a": 0.0 }, "117120": { "creation_time": 1779714836375, "p": [ 23178.3671875, 18315.451171875, 65251.30859375 ], "wind_a": 0.0 }, "117121": { "creation_time": 1779714836375, "p": [ 23122.212890625, 18300.66796875, 65387.25390625 ], "wind_a": 0.0 }, "117122": { "creation_time": 1779714836375, "p": [ 23107.2421875, 18296.7265625, 65540.84375 ], "wind_a": 0.0 }, "117123": { "creation_time": 1779714836375, "p": [ 23135.267578125, 18304.103515625, 65910.0859375 ], "wind_a": 0.0 }, "117124": { "creation_time": 1779714836375, "p": [ 23122.212890625, 18300.66796875, 66058.90625 ], "wind_a": 0.0 }, "117125": { "creation_time": 1779714836375, "p": [ 23044.888671875, 18280.30859375, 66185.78125 ], "wind_a": 0.0 }, "117126": { "creation_time": 1779714836375, "p": [ 22959.03515625, 18257.705078125, 66309.0078125 ], "wind_a": 0.0 }, "117127": { "creation_time": 1779714836375, "p": [ 22959.03515625, 18257.705078125, 66457.828125 ], "wind_a": 0.0 }, "117128": { "creation_time": 1779714836375, "p": [ 22985.14453125, 18264.580078125, 66606.640625 ], "wind_a": 0.0 }, "117129": { "creation_time": 1779714836375, "p": [ 22932.92578125, 18250.83203125, 66744.2734375 ], "wind_a": 0.0 }, "117130": { "creation_time": 1779714836375, "p": [ 22848.4765625, 18228.59765625, 66868.1015625 ], "wind_a": 0.0 }, "117131": { "creation_time": 1779714836375, "p": [ 22821.96484375, 18221.619140625, 66956.265625 ], "wind_a": 0.0 } }, "tags": { "same_wrap_direction": "z" } } } }, "lasagna_base_shape_zyx": [ 75784, 32693, 32693 ], "stages": [ { "lr": 0.1, "min_scaledown": 0, "name": "stage0", "params": [ "mesh_ms" ], "steps": 1000, "w_fac": { "corr": 0.0, "pred_dt": 0.0, "station_n": 10.0, "station_t": 10.0 } }, { "lr": 0.1, "min_scaledown": 0, "name": "stage1", "params": [ "mesh_ms" ], "steps": 1000, "w_fac": { "pred_dt": 0.0, "station_n": 10.0, "station_t": 10.0 } }, { "lr": 0.01, "min_scaledown": 0, "name": "stage2", "params": [ "mesh_ms" ], "steps": 500, "w_fac": { "pred_dt": 0.0, "station_n": 10.0, "station_t": 10.0 } }, { "_lr": [ 10.0, 1.0, 0.1, 0.01, 0.001 ], "args": { "pred_dt_flow_gate": { "anticipatory_pull": { "_debug_roi_center_xyz": [ 17499, 13412, 51144 ], "debug_roi_k": 8, "debug_roi_root_min": 0.5, "debug_roi_tip_max": 0.5, "debug_slice_upsample": 8, "enabled": true, "inlier_one": 120.0, "inlier_zero": 80.0, "loss_weight": 2.0, "samples": 8 }, "backtrack_distance": 50.0, "debug": false, "debug_out_dir": "/home/ubuntu/villa/lasagna", "debug_vis_interval": 0, "enabled": true, "gate_factor": 1.0, "local_boost": 0.5 }, "status_interval": 10 }, "dlr": [ 1.0, 0.1, 0.01, 0.001, 0.0001 ], "lr": 1.0, "min_scaledown": 0, "name": "snap", "params": [ "mesh_ms" ], "steps": 500 } ], "vc3d_volume_shape_zyx": [ 18946, 8174, 8174 ] }, "format": "tifxyz", "lasagna_base_shape_zyx": [ 75784, 32693, 32693 ], "lasagna_job": { "config": { "args": { "corr-point-roi": true, "corr-point-roi-init-margin": 80, "corr-point-roi-output-radius": 20, "init-mode": "shell-dir-crop", "mesh-step": 50.0, "model-h": 5000.0, "model-init": "seed", "model-w": 5000.0, "model-w-unit": "voxels", "seed": [ 5783.81689453125, 4576.02587890625, 16477.521484375 ], "tifxyz-flow-gate-channels": true, "windings": 1 }, "base": { "bend": 100.0, "corr": 0.0001, "data": 0.0, "data_plain": 0.0, "ext_offset": 0.0, "normal": 1.0, "pred_dt": 0.001, "smooth": 10.0, "station_n": 0.1, "station_t": 0.1, "step": 10.0, "winding_density": 0.01 }, "corr_points": { "collections": { "985": { "color": [ 0.250980406999588, 1.0, 0.6274510025978088 ], "metadata": { "winding_is_absolute": true }, "name": "same_wrap2691", "points": { "117115": { "creation_time": 1779714836375, "p": [ 5831.138671875, 4588.48486328125, 16148.48046875 ], "wind_a": 0.0 }, "117116": { "creation_time": 1779714836375, "p": [ 5831.138671875, 4588.48486328125, 16168.48046875 ], "wind_a": 0.0 }, "117117": { "creation_time": 1779714836375, "p": [ 5824.611328125, 4586.7666015625, 16205.685546875 ], "wind_a": 0.0 }, "117118": { "creation_time": 1779714836375, "p": [ 5815.8349609375, 4584.45556640625, 16241.92578125 ], "wind_a": 0.0 }, "117119": { "creation_time": 1779714836375, "p": [ 5805.7900390625, 4581.81103515625, 16277.623046875 ], "wind_a": 0.0 }, "117120": { "creation_time": 1779714836375, "p": [ 5794.591796875, 4578.86279296875, 16312.8271484375 ], "wind_a": 0.0 }, "117121": { "creation_time": 1779714836375, "p": [ 5780.55322265625, 4575.1669921875, 16346.8134765625 ], "wind_a": 0.0 }, "117122": { "creation_time": 1779714836375, "p": [ 5776.810546875, 4574.181640625, 16385.2109375 ], "wind_a": 0.0 }, "117123": { "creation_time": 1779714836375, "p": [ 5783.81689453125, 4576.02587890625, 16477.521484375 ], "wind_a": 0.0 }, "117124": { "creation_time": 1779714836375, "p": [ 5780.55322265625, 4575.1669921875, 16514.7265625 ], "wind_a": 0.0 }, "117125": { "creation_time": 1779714836375, "p": [ 5761.22216796875, 4570.0771484375, 16546.4453125 ], "wind_a": 0.0 }, "117126": { "creation_time": 1779714836375, "p": [ 5739.7587890625, 4564.42626953125, 16577.251953125 ], "wind_a": 0.0 }, "117127": { "creation_time": 1779714836375, "p": [ 5739.7587890625, 4564.42626953125, 16614.45703125 ], "wind_a": 0.0 }, "117128": { "creation_time": 1779714836375, "p": [ 5746.2861328125, 4566.14501953125, 16651.66015625 ], "wind_a": 0.0 }, "117129": { "creation_time": 1779714836375, "p": [ 5733.2314453125, 4562.7080078125, 16686.068359375 ], "wind_a": 0.0 }, "117130": { "creation_time": 1779714836375, "p": [ 5712.119140625, 4557.1494140625, 16717.025390625 ], "wind_a": 0.0 }, "117131": { "creation_time": 1779714836375, "p": [ 5705.4912109375, 4555.40478515625, 16739.06640625 ], "wind_a": 0.0 } }, "tags": { "same_wrap_direction": "z" } } } }, "stages": [ { "lr": 0.1, "min_scaledown": 0, "name": "stage0", "params": [ "mesh_ms" ], "steps": 1000, "w_fac": { "corr": 0.0, "pred_dt": 0.0, "station_n": 10.0, "station_t": 10.0 } }, { "lr": 0.1, "min_scaledown": 0, "name": "stage1", "params": [ "mesh_ms" ], "steps": 1000, "w_fac": { "pred_dt": 0.0, "station_n": 10.0, "station_t": 10.0 } }, { "lr": 0.01, "min_scaledown": 0, "name": "stage2", "params": [ "mesh_ms" ], "steps": 500, "w_fac": { "pred_dt": 0.0, "station_n": 10.0, "station_t": 10.0 } }, { "_lr": [ 10.0, 1.0, 0.1, 0.01, 0.001 ], "args": { "pred_dt_flow_gate": { "anticipatory_pull": { "_debug_roi_center_xyz": [ 17499, 13412, 51144 ], "debug_roi_k": 8, "debug_roi_root_min": 0.5, "debug_roi_tip_max": 0.5, "debug_slice_upsample": 8, "enabled": true, "inlier_one": 120.0, "inlier_zero": 80.0, "loss_weight": 2.0, "samples": 8 }, "backtrack_distance": 50.0, "debug": false, "debug_out_dir": "/home/ubuntu/villa/lasagna", "debug_vis_interval": 0, "enabled": true, "gate_factor": 1.0, "local_boost": 0.5 }, "status_interval": 10 }, "dlr": [ 1.0, 0.1, 0.01, 0.001, 0.0001 ], "lr": 1.0, "min_scaledown": 0, "name": "snap", "params": [ "mesh_ms" ], "steps": 500 } ] }, "linked_surfaces": [], "model": null, "volume_shape_zyx": [ 18946, 8174, 8174 ] }, "model_source": "/tmp/fit_reopt_4uf6zhkn/model_reopt.pt", "scale": [ 0.07999999821186066, 0.07999999821186066 ], "tags": { "date_last_modified": "20260614185644606", "reviewed": { "date": "20260604080934287" } }, "type": "seg", "uuid": "same_wrap002691_lasagna" }